He was also aboard the Planter on December 1, 1863, when the ship came under Confederate fire near Secessionville. The white captain, James Nickerson, according to the accounts, ordered the ship surrendered and attempted to beach it. Smalls refused. His reported reasoning was direct and pragmatic: he believed that if they surrendered, the Black crew members would not be treated as prisoners of war. The alternative — death rather than capture — had a specific meaning in the context of Confederate treatment of captured Black Union soldiers, which had by late 1863 become a documented pattern. He took command of the vessel and piloted it out of range of the Confederate guns.
Following this action, General Quincy Adams Gillmore recognized Smalls’s command and reportedly made him acting captain of the Planter. He is described in multiple accounts as the first African American to command a United States ship, a distinction that reflects both the extraordinary nature of his wartime service and the constraints of the context: the formal status of his various wartime roles, whether as civilian pilot or military officer, has been debated by historians, and the line between these categories was not always clearly maintained during the conflict.
He was present at what he later described as seventeen major engagements. He transported the troops who would fight at Simmons Bluff, participated in operations around Fort Pulaski and Morris Island, and supported General William T. Sherman’s army at Savannah in December 1864. In April 1865, he brought the Planter back to Charleston for the flag-raising ceremony at Fort Sumter, carrying African Americans who had made the journey to witness the moment.